2000 v6 missing on #1

That part you are referring to as a valve is an EGR port where exhaust gas is injected into the cylinder. It is possible that the clogged EGR port is causing the misfire. Since the lower intake manifold is out the EGR passage ways can be cleaned out. There are some small core plugs that will need to come out to clean it out. I've usually had a machine shop do that.

Other things to check for the misfire are spark plugs and wires. The fuel injector and injector pulse (check with a noid light) and compression.